GenPress: A Novel Dictionary Based Method to Compress DNA Data of Various Species

Lehotay-Kéry, Péter; Kiss, Attila

doi:10.1007/978-3-030-14802-7_33

Cited by 3 publications

(2 citation statements)

References 12 publications

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“…The fax transmission implementation also uses RLE and Huffman coding together [14]. While the idea of encoding the RLE runs with Huffman codes is already known and analyzed [22], it is mostly in a static sense and optimized for special purpose applications such as fax transmission and DNA sequences [3,17]. However, the vertical byte reading enables new approaches, even more in combination with the idea of byte remapping and becomes applicable to more than just binary fax or DNA sequences, with longer runs of any kind in average.…”

Section: Combination With Other Compression Methodsmentioning

confidence: 99%

Improving Run Length Encoding by Preprocessing

Sven

Wolf

2021

2021 Data Compression Conference (DCC)

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The Run Length Encoding (RLE) compression method is a long standing simple lossless compression scheme which is easy to implement and achieves a good compression on input data which contains repeating consecutive symbols. In its pure form RLE is not applicable on natural text or other input data with short sequences of identical symbols. We present a combination of preprocessing steps that turn arbitrary input data in a byte-wise encoding into a bit-string which is highly suitable for RLE compression. The main idea is to first read all most significant bits of the input byte-string, followed by the second most significant bit, and so on. We combine this approach by a dynamic byte remapping as well as a Burrows-Wheeler-Scott transform on a byte level. Finally, we apply a Huffman Encoding on the output of the bit-wise RLE encoding to allow for more dynamic lengths of code words encoding runs of the RLE. With our technique we can achieve a lossless average compression which is better than the standard RLE compression by a factor of 8 on average. KeywordsLossless data compression • Vertical byte reading • Run length encoding • Burrows-Wheeler-Scott transform • Dynamic byte remapping • Huffman encoding

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Section: Combination With Other Compression Methodsmentioning

confidence: 99%

Improving Run Length Encoding by Preprocessing

Sven

Wolf

2021

2021 Data Compression Conference (DCC)

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“…Statistical compression methods utilize statistical models to achieve compression [9], [12]. Dictionary-based compression methods use a dictionary of sequences to replace repeated sequences in the data [13], [14], [15], [16]. Reference-based compression, on the other hand, leverages the high interredundancy between chromosomes of the same species by storing the differences between the original sequence and a suitable reference sequence [17], [18], [19], [20], [21], [22].…”

Section: Introductionmentioning

confidence: 99%